MolNFT v1 · #10553 · protein
Structure of 2C-methyl-D-erythritol-2,4-cyclodiphosphate synthase
1IV1 · 2-C-methyl-D-erythritol 2,4-cyclodiphosphate synthase: “Structure of 2C-methyl-D-erythritol-2,4-cyclodiphosphate synthase”. X-ray diffraction, 8 pockets (best druggability 0.77). MolNFT v1 #10553 on GenesisL1: 3D structure, binding…
- PDB
- 1IV1
- Type
- protein
- Length
- 900 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- 2-C-methyl-D-erythritol 2,4-cyclodiphosphate synthase
- EC
- 4.6.1.12
- UniProt
- Q8RQP5
- Pockets
- 8 · best druggability 0.77
Structure
x-ray diffraction · 1 distinct chain · 32% helix, 31% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, C, D, B, E, F | 2-C-methyl-D-erythritol 2,4-cyclodiphosphate synthase (EC 4.6.1.12) | protein | 150 | 32% helix, 31% strand | Q8RQP5 |
Pockets
8 pockets found on a 1 Å grid, 7 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 175 | 0.77 | 0.93 | 36 | empty |
| 2 | 172 | 0.76 | 0.93 | 37 | empty |
| 3 | 975 | 0.74 | 0.77 | 86 | empty |
| 4 | 349 | 0.60 | 0.77 | 33 | empty |
| 5 | 316 | 0.58 | 0.77 | 32 | empty |
Interfaces
9 interfaces between chains.
- B–E · 1017 Ų buried · 24 hydrogen bonds · protein-protein
- C–D · 1006 Ų buried · 19 hydrogen bonds · protein-protein
- A–C · 1005 Ų buried · 20 hydrogen bonds · protein-protein
- B–F · 994 Ų buried · 20 hydrogen bonds · protein-protein
- A–D · 990 Ų buried · 21 hydrogen bonds · protein-protein
Compared structures
- 1IV1 · Structure of 2C-Methyl-D-erythritol-2,4-cyclodiphosphate Synthase · the same entry in another collection · chain D against D, TM-score 1.00
- Q8RQP5 · AlphaFold monomer V2.0 prediction for 2-C-methyl-D-erythritol 2,4-cyclodiphosphate… · a predicted model of the same protein · chain A against A, TM-score 1.00
Analyse
- Open in the research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides and crosslinks on the 3D structure
- Every structure of UniProt Q8RQP5
- Elsewhere: RCSB PDB 1IV1 · PDBe 1IV1 · UniProt Q8RQP5
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